public string GetTabSeparatedHeader()
{
var sb = new StringBuilder();
sb.Append("Protein Accession" + '\t');
sb.Append("Gene" + '\t');
sb.Append("Organism" + '\t');
sb.Append("Protein Full Name" + '\t');
sb.Append("Protein Unmodified Mass" + '\t');
sb.Append("Number of Proteins in Group" + '\t');
sb.Append("Unique Peptides" + '\t');
sb.Append("Shared Peptides" + '\t');
sb.Append("Number of Peptides" + '\t');
sb.Append("Number of Unique Peptides" + '\t');
sb.Append("Sequence Coverage Fraction" + '\t');
sb.Append("Sequence Coverage" + '\t');
sb.Append("Sequence Coverage with Mods" + '\t');
sb.Append("Modification Info List" + "\t");
if (FilesForQuantification != null)
{
bool unfractionated = FilesForQuantification.Select(p => p.Fraction).Distinct().Count() == 1;
bool conditionsUndefined = FilesForQuantification.All(p => string.IsNullOrEmpty(p.Condition));
// this is a hacky way to test for SILAC-labeled data...
// Currently SILAC will report 1 column of intensities per label per spectra file, and is NOT summarized
// into biorep-level intensity values. the SILAC code uses the "condition" field to organize this info,
// even if the experimental design is not defined by the user. So the following bool is a way to distinguish
// between experimental design being used in SILAC automatically vs. being defined by the user
bool silacExperimentalDesign = FilesForQuantification.Any(p => !File.Exists(p.FullFilePathWithExtension));
foreach (var sampleGroup in FilesForQuantification.GroupBy(p => p.Condition))
{
foreach (var sample in sampleGroup.GroupBy(p => p.BiologicalReplicate).OrderBy(p => p.Key))
{
if ((conditionsUndefined && unfractionated) || silacExperimentalDesign)
{
// if the data is unfractionated and the conditions haven't been defined, just use the file name as the intensity header
sb.Append("Intensity_" + sample.First().FilenameWithoutExtension + "\t");
}
else
{
// if the data is fractionated and/or the conditions have been defined, label the header w/ the condition and biorep number
sb.Append("Intensity_" + sample.First().Condition + "_" + (sample.First().BiologicalReplicate + 1) + "\t");
}
}
}
}
sb.Append("Number of PSMs" + '\t');
sb.Append("Protein Decoy/Contaminant/Target" + '\t');
sb.Append("Protein Cumulative Target" + '\t');
sb.Append("Protein Cumulative Decoy" + '\t');
sb.Append("Protein QValue" + '\t');
sb.Append("Best Peptide Score" + '\t');
sb.Append("Best Peptide Notch QValue");
return(sb.ToString());
}
public string GetTabSeparatedHeader()
{
var sb = new StringBuilder();
sb.Append("Protein Accession" + '\t');
sb.Append("Gene" + '\t');
sb.Append("Organism" + '\t');
sb.Append("Protein Full Name" + '\t');
sb.Append("Protein Unmodified Mass" + '\t');
sb.Append("Number of Proteins in Group" + '\t');
sb.Append("Unique Peptides" + '\t');
sb.Append("Shared Peptides" + '\t');
sb.Append("Number of Peptides" + '\t');
sb.Append("Number of Unique Peptides" + '\t');
sb.Append("Sequence Coverage Fraction" + '\t');
sb.Append("Sequence Coverage" + '\t');
sb.Append("Sequence Coverage with Mods" + '\t');
sb.Append("Modification Info List" + "\t");
if (FilesForQuantification != null)
{
bool unfractionated = FilesForQuantification.Select(p => p.Fraction).Distinct().Count() == 1;
bool conditionsDefined = FilesForQuantification.All(p => p.Condition == "Default") || FilesForQuantification.All(p => string.IsNullOrWhiteSpace(p.Condition));
foreach (var sampleGroup in FilesForQuantification.GroupBy(p => p.Condition))
{
foreach (var sample in sampleGroup.GroupBy(p => p.BiologicalReplicate).OrderBy(p => p.Key))
{
if (!conditionsDefined && unfractionated)
{
// if the data is unfractionated and the conditions haven't been defined, just use the file name as the intensity header
sb.Append("Intensity_" + sample.First().FilenameWithoutExtension + "\t");
}
else
{
// if the data is fractionated and/or the conditions have been defined, label the header w/ the condition and biorep number
sb.Append("Intensity_" + sample.First().Condition + "_" + (sample.First().BiologicalReplicate + 1) + "\t");
}
}
}
}
sb.Append("Number of PSMs" + '\t');
sb.Append("Protein Decoy/Contaminant/Target" + '\t');
sb.Append("Protein Cumulative Target" + '\t');
sb.Append("Protein Cumulative Decoy" + '\t');
sb.Append("Protein QValue" + '\t');
sb.Append("Best Peptide Score" + '\t');
sb.Append("Best Peptide Notch QValue");
return(sb.ToString());
}